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Phylogenetic Factorization of Mammalian Viruses Complements Trait- Based Analyses and Guides Surveillance Efforts

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Phylogenetic Factorization of Mammalian Viruses Complements Trait- Based Analyses and Guides Surveillance Efforts bioRxiv preprint doi: https://doi.org/10.1101/267252; this version posted February 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Phylogenetic factorization of mammalian viruses complements trait- based analyses and guides surveillance efforts Alex D. Washburne1*, Daniel E. Crowley1, Daniel J. Becker1,2, Kevin J. Olival3, Matthew Taylor1, Vincent J. Munster4, Raina K. Plowright1 1Department of Microbiology and Immunology, Montana State University, Bozeman MT 2Center for the Ecology of Infectious Disease, University of Georgia, Athens, GA 3EcoHealth Alliance New York, NY 4National Institute of Allergy and Infectious Diseases, Hamilton, MT *Corresponding author: [email protected] Abstract Predicting which novel microorganisms may spill over from animals to humans has become a major priority in infectious disease biology. However, there are few tools to help assess the zoonotic potential of the enormous number of potential pathogens, the majority of which are undiscovered or unclassified and may be unlikely to infect or cause disease in humans. We adapt a new biological machine learning technique - phylofactorization - to partition viruses into clades based on their non-human host range and whether or not there exist evidence they have infected humans. Our cladistic analyses identify clades of viruses with common within-clade patterns - unusually high or low propensity for spillover. Phylofactorization by spillover yields many clades of viruses containing few to no representatives that have spilled over to humans, including the families Papillomaviridae and Herpesviridae, and the genus Parvovirus. Removal of these non-zoonotic clades from previous trait-based analyses changed the relative significance of traits determining spillover due to strong associations of traits with non-zoonotic clades. Phylofactorization by host breadth yielded clades with unusually high host breadth, including the family Togaviridae. We identify putative life-history traits differentiating clades’ host breadth and propensities for zoonosis, and discuss how these results can prioritize sequencing-based surveillance of emerging infectious diseases. Introduction Zoonotic spillover, the transmission of pathogens from non-human vertebrate animals to humans, is a major public health challenge yet the prediction and management of which pathogens spillover is poorly understood (Plowright et al. 2017). Recent, high-profile spillover events, such as that of Nipah virus (Chua et al. 2000; Pulliam et al. 2012), Hendra virus (Murray et al. 1995; Plowright et al. 2015), avian influenza virus (Fouchier et al. 2004; Li et al. 2014), Ebola virus (Baize et al. 2014), rabies virus (Messenger, Smith, and Rupprecht 2002; Schneider et al. 2009), Chikungunya virus (Powers and Logue 2007), Zika virus (Wikan and Smith 2016), and West Nile virus (Petersen and Roehrig 2001; Hayes and Gubler 2006), among others, strongly motivate a broader understanding of the trait determinants and viral clades at risk of pathogen spillover (Rosenberg 2015; Geoghegan et al. 2016; Plowright et al. 2016; Geoghegan and Holmes 2017; Lloyd-Smith et al. 2009). bioRxiv preprint doi: https://doi.org/10.1101/267252; this version posted February 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Emerging infectious diseases arise from a pre-existing pool of viruses with traits, life- histories, and evolutionary histories, all of which interact to determine the propensity for pathogen spillover. With thousands of viruses in nature, understanding which clades of viruses are most prone to zoonotic spillover is critical for improving pathogen surveillance efforts and designing public health interventions across scales from reservoir hosts to humans. A recent study examined viral traits that predicted a virus' zoonotic status; after controlling for research effort they found that predictors included the phylogenetic host breadth of the virus, genome length, and whether or not the virus was vector borne, reproduced in the cytoplasm, or was enveloped (Olival et al. 2017). Trait-based analyses such as these are insightful and useful, but can be limited by incomplete characterization of traits associated with zoonoses and confounded or biased by entire clades of pathogens that are non-zoonotic and whose homologous traits can all become negatively associated with zoonosis. Cladistic analyses complement trait-based analyses by identifying monophyletic clades or taxonomic groups with common patterns of zoonosis (Figure 1). Cladistic analyses can enhance and focus trait-based analyses to refine an understanding of the causes of viral zoonoses. Viral life histories - the patterns and traits determining survival and reproduction - vary greatly across lineages with vastly different molecular machinery for host cell entry, viral gene expression, replication, assembly and dissemination (Jane Flint et al. 2015). General traits, such genetic material or presence of an envelope, may miss the specific molecular mechanisms, such as promiscuous receptor binding or immunoevasion, by which viral quasispecies from a particular clade can become capable of infecting humans. Furthermore, general traits found across all viruses may be less actionable for management interventions than clade-specific mechanisms. For example, knowing the particular species of mosquito, Aedes aegypti, responsible for transmitting many Flaviviruses (Black et al. 2002) enables ecological interventions aimed at modifying A. aegypti susceptibility to Flavivirus infection, population density, and more (Morrison et al. 2008). Identifying viral clades with unusually high or low propensity for spillover can prioritize surveillance effort and generate detailed, clade-specific hypotheses about molecular mechanisms and pathogen life- history traits driving spillover risk. Furthermore, identification of non-zoonotic clades can allow refined trait-based analyses: instead of “which traits are associated with zoonosis”, one can ask “which traits are associated with zoonosis for those pathogens at risk of spilling over?” Identifying molecular mechanisms and hypothesized life-history traits for clade-specific determinants of spillover can revise the list of explanatory traits in trait-based analyses (Figure 1). To build off the recent study of viral traits determining spillover, we apply a new biological machine-learning method, phylofactorization (A. D. Washburne, Silverman, Leff, et al. 2017; A. D. Washburne, Silverman, Morton, et al. 2017), to identify clades of mammalian viruses with high within-clade similarity in zoonotic potential and high between-clade differences. Phylofactorization is a graph-partitioning algorithm that partitions a tree, in our case the International Committee on Taxonomy of Viruses (ICTV) taxonomy tree, by identifying edges with the most significant differences in the response variable. Using a cladistic taxonomy tree as a scaffold for identifying clades with common propensities for spillover can flexibly identify the range of taxonomic scales of interest and implicitly identify life history traits which enable viruses to spill over into humans. We analyze viruses from a recently published dataset bioRxiv preprint doi: https://doi.org/10.1101/267252; this version posted February 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. of mammalian viruses (Olival et al. 2017) and replicate the paper’s trait-based analysis alongside our cladistic analysis to provide a side-by-side comparison of how a cladistic analysis informs, complements and, in some cases, changes the results of trait-based analyses. We perform phylofactorization by whether or not a clade has infected humans, discover several non-zoonotic clades, and remove the non-zoonotic clades from a replicated trait-based analysis. We then perform phylofactorization by non-human host breadth, as it is a related measurement of the host-tropism of viruses and a robust predictor of whether/not a virus can infect humans. Host-breadth phylofactorization yields a set of clades with high host breadth and high propensity to spillover. Having identified non-zoonotic clades and clades with high non- human host breadth and a high risk of zoonosis, we finish with a discussion of the life-histories of two somewhat opposite clades on the spectrum of spillover risk: the families Togaviridae and Herpesviridae. The life-history discussion is used to motivate a level of molecular and mechanistic detail which can enable clade-specific surveillance and management of pathogen spillover. Results Zoonotic Phylofactorization & Comparative trait-based analysis Phylofactorization of whether or not a virus is zoonotic yielded 10 significant clades of various sizes and taxonomic levels (Figure 2). The viral family Papillomaviridae, family Herpesviridae, subfamily Orthoretrovirinae, order Nidovirales, genus Parvovirus, and families Calciviridae, Adenoviridae, and Astroviridae all had a lower fraction of zoonotic representatives
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